Variant report

Variant	rs62165196
Chromosome Location	chr2:55801791-55801792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55746047..55748264-chr2:55800311..55802508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10454749	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10496050	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1058582	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1084522	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11125579	0.86[EUR][1000 genomes]
rs11125581	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17278044	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17369191	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17798852	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1823893	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1975484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1975487	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054728	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2586947	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2586968	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586969	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586970	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2627759	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2627776	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627777	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627780	0.81[AMR][1000 genomes]
rs2627782	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35504023	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762513	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4290693	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4312532	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4672052	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4672054	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4672055	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4672056	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55761024	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58003472	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62165173	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62165181	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62165182	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62165183	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62165184	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165197	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62165200	0.80[AFR][1000 genomes]
rs6545506	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739513	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7582278	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7594279	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7598650	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782586	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs782587	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782588	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782590	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs782594	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782595	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782599	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782600	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782601	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782602	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782613	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs782649	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782650	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782652	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs935177	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62165196	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
4	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55770800-55815800	Strong transcription	Liver	Liver
6	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:55785000-55805000	Weak transcription	NHEK	skin
10	chr2:55788600-55816600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:55788800-55808200	Weak transcription	Right Ventricle	heart
12	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:55789600-55804800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:55789800-55802600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:55789800-55808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
17	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55790200-55812800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
21	chr2:55790400-55808800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
23	chr2:55790800-55816600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:55791200-55812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:55791400-55805800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:55792000-55804000	Weak transcription	K562	blood
28	chr2:55792000-55806000	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:55793200-55805200	Weak transcription	NHDF-Ad	bronchial
30	chr2:55793400-55817000	Strong transcription	Fetal Thymus	thymus
31	chr2:55794200-55808000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:55794200-55808800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:55794200-55818200	Weak transcription	Psoas Muscle	Psoas
34	chr2:55794400-55805000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:55794400-55812200	Weak transcription	NHLF	lung
36	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:55794600-55802400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:55794800-55802400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:55794800-55802400	Weak transcription	Brain Anterior Caudate	brain
41	chr2:55794800-55804800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:55794800-55805800	Weak transcription	Fetal Kidney	kidney
43	chr2:55794800-55816200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:55795000-55807200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:55795200-55803800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:55795200-55805200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:55795400-55802400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:55795400-55807800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:55795600-55806800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:55796000-55802400	Weak transcription	A549	lung

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